From patchwork Fri May 21 20:25:47 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29461 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 1FB6727BC78; Fri, 21 May 2021 21:28:30 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 8180E27BC81 for ; Fri, 21 May 2021 21:28:29 +0100 (BST) Received: from localhost ([::1]:36948 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBky-0005aV-ME for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:28:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52442) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkd-0004VW-Br for guix-patches@gnu.org; Fri, 21 May 2021 16:28:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54493) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkd-0002x9-2f for guix-patches@gnu.org; Fri, 21 May 2021 16:28:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkc-0000Mf-Vq for guix-patches@gnu.org; Fri, 21 May 2021 16:28:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288461028 (code B ref 48575); Fri, 21 May 2021 20:28:06 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:26 +0000 Received: from localhost ([127.0.0.1]:37725 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjy-0000GP-AI for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:26 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:51727) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjL-00008k-QJ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:48 -0400 Received: by mail-wm1-f45.google.com with SMTP id u133so11744821wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=ePOu/WOmhRx9vzCfP9R7pDT0sp4w/OutgjJuExwrTy0=; b=DOcAeEW8GgDzRYazjzSs17nd1ySJK736St39aoiXWdZogOjNGv6ESWCKf9gAzDEKDe n450KyIgHO19LPwLcXNaXEneLsQHASvdsd59JTaxv8r75IZ9TWYN5VTkebH0j2PFGVgw VMPGXS/VpxHnV7zg3qmoV1bP15HjxMPe7HKxV4o6YCY2+WwiuA+QkQ78H1PNcJx/wqsO SqctMDcjBLi70GsLGpsK4wlnfO/6tsz/nTOmN1eLEKFj7CDGvSex0WhnyVjC/mHZx2TX AAX86g6bHhERFbkrXcLJSw3L8iFyqbgLow/yRbJsoFdeRJ4TpMn9K0xiPPKmkz9WKmu2 nz6Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=ePOu/WOmhRx9vzCfP9R7pDT0sp4w/OutgjJuExwrTy0=; b=nYMK05Hp3Pq0NC1jsdZZ5b9A33oD9ETh3vDpz53YjGhHH3DpIk5TKgWTqsEWlP4AT3 NiXkLFU7V3tbJLLIJadG7Jr7hhILDHeWirfA9u5jnNDP+uj2AWzB5p6BKNREBp/vFZJo BOk019Y/v1AxvqvAYaxHnv81LOBLJij5vW1H1/F85NhDfiPpKlqzZgu8l2XI2SFMV63z ctyNjv13JjyQcttC6Svh+JSMRdYw55NVJJJNLg/FoLDVj41eDf46S2+vJ+taOa+hWE5b Zgoi5EjosWTLEYCW+SAxFESVANssqp5sOaL85rPLdp7Ozd8SVdpE6DoNDSDyYb983cZb raDw== X-Gm-Message-State: AOAM533aFwpj4G95hhG45yOFrql/GCBFuAlnxZPP/T2Bwwg93tpWbhLH +J0n1ufJ2kBottamS3eFlNQEhNIPc10= X-Google-Smtp-Source: ABdhPJxOoaKGHLY1upRxZzX4NwrhGC33iemyoiQXxzXM3vTnywP9AHuQv/L5TeUewj4jXu53LBPCZQ== X-Received: by 2002:a1c:c911:: with SMTP id f17mr10438184wmb.45.1621628802273; Fri, 21 May 2021 13:26:42 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:42 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:47 +0200 Message-Id: <20210521202622.26591-15-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-mzid): Move from here... * gnu/packages/bioconductor.scm (r-mzid): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1533e5b8f9..5e0b722e2f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2526,6 +2526,37 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-mzid + (package + (name "r-mzid") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzID" version)) + (sha256 + (base32 + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) + (properties `((upstream-name . "mzID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/mzID") + (synopsis "Parser for mzIdentML files") + (description + "This package provides a parser for mzIdentML files implemented using the +XML package. The parser tries to be general and able to handle all types of +mzIdentML files with the drawback of having less pretty output than a vendor +specific parser.") + (license license:gpl2+))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a98f3d5d8a..5b6426e17d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-mzid - (package - (name "r-mzid") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzID" version)) - (sha256 - (base32 - "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) - (properties `((upstream-name . "mzID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/mzID") - (synopsis "Parser for mzIdentML files") - (description - "This package provides a parser for mzIdentML files implemented using the -XML package. The parser tries to be general and able to handle all types of -mzIdentML files with the drawback of having less pretty output than a vendor -specific parser.") - (license license:gpl2+))) - (define-public r-aroma-light (package (name "r-aroma-light")